Structural Superimposition of Local Sequence Alignment

GUNGOR BUDAK, 1720184, Bioinformatics MSc, Middle East Technical University

A program which finds out whether a local sequence alignment of two protein sequences also implies structural similarity of the aligned parts.

Arguments

1. First PDB ID – no default value, must be given
2. Second PDB ID – no default value, must be given
3. Gap open penalty (a nonpositive number) – default: -10
4. Gap extension penalty (a nonpositive number) – default: -5

Requirements

• Python 2.7.x
• NumPy 1.9.1
• BioPython 1.64

Usage

D:\projects\sslsa>python sslsa.py 1xyx 1xu0
Downloading PDB structure '1xyx'...
Downloading PDB structure '1xu0'...
LGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPV---DQYSNQNNFVHDCVNITIKQHTVTTTTKGEN--FT
ETDVKMMERVVEQMCVTQYQKES
IGGYMLGNAVGRMSYQFNNPMESRYYNDYYNQMPNRVY-RPMYRGEEYVSEDRFVRDCYNMSVTEYIIKPAEGKNNSELN
QLDTTVKSQIIREMCITEYRRGS
Alignment length: 103
RMSD: 2.87702543237

or

D:\projects\sslsa>python sslsa.py 1xyx 1xu0 -5 -5
Downloading PDB structure '1xyx'...
Downloading PDB structure '1xu0'...
LGGYMLGSAMSRPMIHFGNDWEDRYYRENMY-RYPNQVYYRPV---DQYSNQNNFVHDCVNITIKQHTVTTTTKGENFTE
-T--DVKMMERVVEQMCVTQYQKES
IGGYMLGNAVGRMSYQFNNPMESRYYND-YYNQMPNRVY-RPMYRGEEYVSEDRFVRDCYNMSVTEYIIKPA-EGKNNSE
LNQLDTTVKSQIIREMCITEYRRGS
Alignment length: 105
RMSD: 2.96977891523

Interpretation

Similar sequences yield similar lower RMSD because they are actually similar but since several amino acids can be grouped according to their structural properties, even if the sequences might not be very similar we might get lower RMSD due to structural biochemical similarity. This shows that structure is more conserved during the course of evolution, whereas sequences are subject to changes due to the mechanisms of evolution such as mutation, genetic drift, gene flow.